Burhan Sahyouni gave Syria the lead in the 47th minute.
Jordan’s Musab Al Lahham levelled with a header in the 57th minute.
The result enables Jordan to keep its unbeaten streak in the qualifiers for a place in the finals in Australia in 2015.
Jordan is now second in Group A with four points, two less than Oman, which defeated Singapore 2-0 on Wednesday.
Syria is third with only one point, while Singapore is at the bottom of the table with no points.
The game was played in Tehran due to the ongoing unrest in Syria.